Contacts of the strand formed by residues 552 - 558 (chain I) in PDB entry 1DE4
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with ALA 552 (chain I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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481I TYR* 3.2 22.0 - - + +
498I ALA* 3.0 4.9 - - - +
499I SER* 3.0 28.2 + - - -
502I LEU* 3.6 4.3 - - - +
535I LEU* 4.4 4.4 - - + +
541I ALA* 3.7 33.7 - - + +
544I PHE* 4.1 1.3 - - + -
545I LEU* 4.3 7.9 - - + +
550I ILE 3.0 8.6 + - - +
551I PRO* 1.3 75.2 - - - +
553I VAL* 1.3 61.0 + - - +
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Residues in contact with VAL 553 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
481I TYR 3.0 12.9 + - - +
482I ILE* 3.9 25.1 - - + -
483I ASN* 3.0 28.9 + - - +
496I VAL* 4.7 1.8 - - + -
497I SER 3.4 2.9 - - - +
498I ALA* 3.4 22.0 - - + -
502I LEU* 3.6 15.0 - - + -
506I ILE* 3.7 19.5 - - + -
541I ALA* 4.2 4.4 - - - +
552I ALA* 1.3 75.2 - - - +
554I SER* 1.3 74.1 + - - +
555I PHE* 4.9 1.8 - - + -
597I PHE* 4.3 20.9 - - + -
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Residues in contact with SER 554 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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483I ASN* 4.4 14.3 + - - +
485I ASP 4.9 5.9 + - - -
496I VAL* 3.5 0.9 - - - -
497I SER* 2.8 37.6 + - - +
535I LEU* 4.4 6.5 - - - -
539I ASN* 3.1 37.1 + - - -
553I VAL* 1.3 78.0 - - - +
555I PHE* 1.3 69.9 + - - +
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Residues in contact with PHE 555 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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482I ILE* 4.4 11.4 - - + -
483I ASN 4.2 17.1 + - - +
484I LEU* 4.2 11.6 - - + -
485I ASP 4.6 2.8 - - - +
486I LYS 4.4 1.0 - - - +
487I ALA* 3.6 18.2 - - + +
494I PHE* 3.8 14.8 - + + -
495I LYS 3.3 6.3 - - - +
496I VAL* 3.4 23.1 - - + +
553I VAL* 4.9 2.2 - - + -
554I SER* 1.3 85.2 + - - +
556I CYS* 1.3 70.3 + - - +
557I PHE* 5.3 0.7 - + - -
590I ALA* 3.7 27.8 - - + -
593I VAL* 3.3 32.8 - - + -
594I ALA* 4.2 9.0 - - + -
597I PHE* 4.0 23.8 - + - -
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Residues in contact with CYS 556 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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486I LYS 3.4 17.0 - - - +
487I ALA 3.1 14.1 - - - +
489I LEU* 4.9 5.6 - - + -
494I PHE* 3.0 12.3 - - - -
495I LYS* 3.0 36.7 + - - -
555I PHE* 1.3 82.0 - - - +
557I PHE* 1.3 65.5 + - - +
558I CYS* 2.1 45.2 - - + -
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Residues in contact with PHE 557 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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487I ALA 2.9 13.8 + - - +
488I VAL* 4.7 0.2 - - - -
489I LEU 2.8 30.3 + - - -
490I GLY 2.8 13.9 + - - +
491I THR* 4.7 8.7 - - - -
493I ASN 3.1 15.3 - - - +
494I PHE* 3.6 30.5 - + + -
514I LYS 5.5 0.4 - - - -
515I HIS* 4.8 3.4 - + - -
516I PRO* 3.7 23.8 - - + -
522I LEU* 3.9 25.1 - - + -
555I PHE* 5.3 0.9 - + - -
556I CYS* 1.3 72.1 - - - +
558I CYS* 1.3 54.5 + - - +
586I VAL* 3.7 31.6 - - + -
589I ALA* 3.6 30.5 - - + -
590I ALA* 3.7 17.7 - - + -
593I VAL* 5.0 0.7 - - + -
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Residues in contact with CYS 558 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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489I LEU* 4.2 12.8 - - + -
490I GLY* 3.8 11.0 - - - +
492I SER 3.8 1.6 + - - -
493I ASN 2.9 27.3 + - - +
495I LYS* 3.2 35.3 + - + +
556I CYS* 2.1 52.7 - - + -
557I PHE* 1.3 74.2 - - - +
559I GLU* 1.3 67.1 + - - +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il